Raquel dos Santos Linheiro

Centre for Biotechnology and Fine Chemistry (CBQF)

Raquel dos Santos Linheiro

rlinheiro@porto.ucp.pt

My PhD thesis entitled ″Computational analyses of transposable element target site preferences in Drosophila melanogaster″ was completed in 2011 and attributed by The University of Manchester (UK).

My main research areas include computational biology, with an extensive use of Statistical Computing language R, as well as Unix, Perl, MySQL and Javascript; molecular biology, more specifically in relation to the analysis of next generation sequencing data (Illumina, 454, SOLiD and PacBio); transposable elements mainly their insertion site preferences and its connection to the host genome properties; and functional biology in relation to promoter regions, gene regulation and synteny areas.

I am currently integrated within the project BioN2Value in the Centro de Biotecnologia e Química Fina da Universidade Católica do Porto. Within this position I conduct the analysis of next generation sequencing data from both metagenomics (identification of different species niches) and isolated organisms (bacteria and plant gene function and identification).

 

Publications:

Nelson MG. Linheiro RS, Bergman C. M.  (2017).  "McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. " G3 (Bethesda) 7(8):2763-2778

Linheiro, R. S. and Bergman C. M. (2012). "Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster." PLoS one 7(2):e30008

Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, Casillas S, Han Y, Magwire MM, Cridland JM, Richardson MF, Anholt RR, Barrón M, Bess C, Blankenburg KP, Carbone MA, Castellano D, Chaboub L, Duncan L, Harris Z, Javaid M, Jayaseelan JC, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P, Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DM, Nazareth L, Newsham I, Perales L, Pu LL, Qu C, Ràmia M, Reid JG, Rollmann SM, Rozas J, Saada N, Turlapati L, Worley KC, Wu YQ, Yamamoto A, Zhu Y, Bergman CM, Thornton KR, Mittelman D, Gibbs RA. (2012) "The Drosophila melanogaster Genetic Reference Panel." Nature 8;482(7384):173-8

Mark F. Richardson, Mike Magwire, Raquel Linheiro, Frank Jiggins, Casey M. Bergman (2012). "Population genomics of the Drosophila melanogaster Wolbachia endosymbiont" PLoS Genetics; 8(12):e1003129

Linheiro, R. S. and Bergman C. M. (2008). "Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element." Nucleic Acids Res 36(19): 6199-208

Researcher Center

Centre for Biotechnology and Fine Chemistry (CBQF)

Academic CV